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- EMDB-11925: Cytochrome c oxidase structure in O-state -

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Basic information

Entry
Database: EMDB / ID: EMD-11925
TitleCytochrome c oxidase structure in O-state
Map datadensity modified map
Sample
  • Complex: Cytochrome c oxidase with four subunits reconstituted in lipid nanodisc
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
KeywordsTerminal oxidase Cytochrome c oxidase aa3 oxidase / MEMBRANE PROTEIN
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. ...Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin
Similarity search - Domain/homology
Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 4 / Cytochrome c oxidase subunit 1-beta
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKolbe F / Safarian S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cytochrome c oxidase structure in O-state
Authors: Kolbe F / Safarian S / Michel H
History
DepositionNov 2, 2020-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7au6
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_11925.map.gz / Format: CCP4 / Size: 10.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdensity modified map
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 1.75 / Movie #1: 1.5
Minimum - Maximum-25.650707000000001 - 47.431956999999997
Average (Standard dev.)0.000000000015018 (±0.5117955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin696735
Dimensions138118165
Spacing118138165
CellA: 98.294 Å / B: 114.954 Å / C: 137.445 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z118138165
origin x/y/z0.0000.0000.000
length x/y/z98.294114.954137.445
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS676935
NC/NR/NS118138165
D min/max/mean-25.65147.4320.000

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Supplemental data

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Sample components

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Entire : Cytochrome c oxidase with four subunits reconstituted in lipid na...

EntireName: Cytochrome c oxidase with four subunits reconstituted in lipid nanodisc
Components
  • Complex: Cytochrome c oxidase with four subunits reconstituted in lipid nanodisc
    • Protein or peptide: Cytochrome c oxidase subunit 1-beta
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 4
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM ION
  • Ligand: OXYGEN MOLECULE
  • Ligand: HYDROGEN PEROXIDE
  • Ligand: MANGANESE (II) ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Cytochrome c oxidase with four subunits reconstituted in lipid na...

SupramoleculeName: Cytochrome c oxidase with four subunits reconstituted in lipid nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 127 KDa

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Macromolecule #1: Cytochrome c oxidase subunit 1-beta

MacromoleculeName: Cytochrome c oxidase subunit 1-beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 62.486645 KDa
SequenceString: MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP ...String:
MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP PLSTTEAGYS MDLAIFAVHV SGASSILGAI NIITTFLNMR APGMTLFKVP LFAWSVFITA WLILLSLPVL AG AITMLLM DRNFGTQFFD PAGGGDPVLY QHILWFFGHP EVYIIILPGF GIISHVISTF AKKPIFGYLP MVLAMAAIGI LGF VVWAHH MYTAGMSLTQ QAYFMLATMT IAVPTGIKVF SWIATMWGGS IEFKTPMLWA FGFLFLFTVG GVTGVVLSQA PLDR VYHDT YYVVAHFHYV MSLGAVFGIF AGVYYWIGKM SGRQYPEWAG QLHFWMMFIG SNLIFFPQHF LGRQGMPRRY IDYPV EFAY WNNISSIGAY ISFASFLFFI GIVFYTLFAG KRVNVPNYWN EHADTLEWTL PSPPPEHTFE TLPKREDWDR AHAH

UniProtKB: Cytochrome c oxidase subunit 1-beta

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Macromolecule #2: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 32.563643 KDa
SequenceString: MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML ...String:
MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML EKEALADAGY SEDEYLLATD NPVVVPVGKK VLVQVTATDV IHAWTIPAFA VKQDAVPGRI AQLWFSVDQE GV YFGQCSE LCGINHAYMP IVVKAVSQEK YEAWLAGAKE EFAADASDYL PASPVKLASA E

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #3: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 30.808174 KDa
SequenceString: MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVLEGD ...String:
MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVLEGD RKTTINGLIV AVILGVCFTG LQAYEYSHAA FGLADTVYAG AFYMATGFHG AHVIIGTIFL FVCLIRLLKG QM TQKQHVG FEAAAWYWHF VDVVWLFLFV VIYIWGR

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #4: Cytochrome c oxidase subunit 4

MacromoleculeName: Cytochrome c oxidase subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 5.509322 KDa
SequenceString:
MASHHEITDH KHGEMDIRHQ QATFAGFIKG ATWVSILSIA VLVFLALANS

UniProtKB: Cytochrome c oxidase subunit 4

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Macromolecule #5: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #6: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 8 / Number of copies: 6 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #9: HYDROGEN PEROXIDE

MacromoleculeName: HYDROGEN PEROXIDE / type: ligand / ID: 9 / Number of copies: 1 / Formula: PEO
Molecular weightTheoretical: 34.015 Da
Chemical component information

ChemComp-PEO:
HYDROGEN PEROXIDE

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Macromolecule #10: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #11: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #12: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 148 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Formula: KPi / Component - Name: Potassium Phosphate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 30.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 321273
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

3hb3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-7au6:
Cytochrome c oxidase structure in O-state

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